Noob question about simple geometry
The simplest solution should be to move the faces along their normal. It's sort of an extrude, but without creating new faces. So you can re-position a face that was previously extruded. To do it, press alt+S. Move the mouse up and down to see the faces move. Click a mouse button when you are satisfied.

One thing that I often do is create a new edge loop that I position where I want it. Then Dissolve the unwanted geometry. If you dissolve it correctly instead of removing it, you won't have to create new faces to fill in any holes. Use ctrl+R to start creating an edge loop. Move the mouse over the geometry to position the edge loop. Click the mouse to continue. Now you can move the edge loop up and down with the mouse. Click again when you are satisfied and you are halfway done. 

Select the geometry you don't want. For instance, right click the outermost face. Type ctrl++ to expand the selection until you have everything selected. Or select using right click while holding down shift. Type x and select "Dissolve faces".